Related papers: On the relation between native geometry and confor…
Many complex structures and stochastic patterns emerge from simple kinetic rules and local interactions, and are governed by scale invariance properties in combination with effects of the global geometry. We consider systems that can be…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
Energy landscape theory describes how a full-length protein can attain its native fold by sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the ribosome,…
We review and further develop an analytical model that describes how thermodynamic constraints on the stability of the native state influence protein evolution in a site-specific manner. To this end, we represent both protein sequences and…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…
We investigate by Molecular-Dynamics simulations the fast mobility - the rattling amplitude of the particles temporarily trapped by the cage of the neighbors - in mildly supercooled states of dense molecular (linear trimers) and atomic…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
Controlling the self-assembly of supramolecular structures is vital for living cells, and a central challenge for engineering at the nano- and microscales. Nevertheless, even particles without optimized shapes can robustly form well-defined…
Geometric constraints impact the formation of a broad range of spatial networks, from amino acid chains folding to proteins structures to rearranging particle aggregates. How the network of interactions dynamically self-organizes in such…
We analytically derive the lower bound of the total conformational energy of a protein structure by assuming that the total conformational energy is well approximated by the sum of sequence-dependent pairwise contact energies. The condition…
We studied the possibility to approximate a Lennard Jones interaction by a pairwise contact potential. First we used a Lennard-Jones potential to design off-lattice, protein-like heteropolymer sequences, whose lowest energy (native)…
How the geometry of nano-sized confinement affects dynamics of biomaterials is interesting yet poorly understood. An elucidation of structural details upon nano-sized confinement may benefit manufacturing pharmaceuticals in biomaterial…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
Paradigmatic model systems, which are used to study the mechanical response of matter, are random networks of point-atoms, random sphere packings, or simple crystal lattices, all of these models assume central-force interactions between…
We describe the results obtained from an improved model for protein folding. We find that a good agreement with the native structure of a 46 residue long, five-letter protein segment is obtained by carefully tuning the parameters of the…
To go beyond the simple model for the fold as two flexible surfaces or faces linked by a crease that behaves as an elastic hinge, we carefully shape and anneal a crease within a polymer sheet and study its mechanical response. First, we…
We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate…
We present the results of a self-consistent, unified molecular dynamics study of simple model heteropolymers in the continuum with emphasis on folding, sequence design and the determination of the interaction parameters of the effective…